You can easily take the train into Como. I have only overnighted there once, and in a hostel, so I can't help you with where to stay. Since you have a night (and part of a day) it might be ideal to go on a boat tour of the lake, its beautiful and you can get off and on wherever you want and explore.
If you just have one night and are tired/want to take it easy, I would rent a car or take a cab (expensive but saves time and hassle). I would actually cab/train it into Milan, get a hotel room and maybe hastily try to arrange to see a an opera or play at La Scala (something I've never done). The hotel could probably arrange it. You could do that and get a great meal, maybe wander around a bit (one of my favorite past times in Italy), and then get a good night's sleep before flying out the next day.